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Hydroxylase homolog of BesD with Fe(II), alpha-ketoglutarate, and lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 In an anaerobic chamber, equal volumes of protein solution (3 mg/mL Hydroxylase, lysine (3 mM), KG (3 mM, pH 7)) and reservoir solution (HEPES pH 7.0 (100 mM), sodium nitrate (200 mM) containing 28% (w/v) PEG 3350); Crystals were soaked with iron chloride before flash freezing
Crystal Properties Matthews coefficient Solvent content 2.58 52.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.626 α = 90 b = 93.53 β = 107.56 c = 91.339 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 194 PIXEL DECTRIS PILATUS3 S 6M 2020-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.111 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 87.081 99.4 0.253 0.2744 0.987 6.2 6.9 40203 38.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.589 1.644 0.519 1.42
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6NIE 2.5 87.08 1.34 40200 1967 99.43 0.1826 0.1802 0.1807 0.2285 0.2291 43.7164
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.23 f_angle_d 0.434 f_chiral_restr 0.041 f_plane_restr 0.003 f_bond_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7831 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 100
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHENIX phasing